Error in picrust2 analysis

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1

Hi everyone,

I am trying to perform picrust2 analysis. The tree had been successfully constructed. The next step, however, has resulted in the following error:

qiime picrust2 custom-tree-pipeline --i-table '/media/sf_compartida/Proyecto/Analisis_primer_seg/Filtrado/birds_primer_seg_table_filtered-ffff.qza' --i-tree '/media/sf_compartida/Proyecto/PICRUST/primer_analis_fragment_pricust--verbose/tree.qza' --output-dir '/media/sf_compartida/Proyecto/PICRUST/q2-picrust2-output-primer' --p-threads 1 --p-hsp-method pic --p-max-nsti 2 --verbose
Running the below commands:
hsp.py -i 16S -t /tmp/tmp31dw214p/placed_seqs.tre -p 1 -n -o /tmp/tmp31dw214p/picrust2_out/16S_predicted.tsv.gz -m pic -e 0.5

Error running this command:
hsp.py -i 16S -t /tmp/tmp31dw214p/placed_seqs.tre -p 1 -n -o /tmp/tmp31dw214p/picrust2_out/16S_predicted.tsv.gz -m pic -e 0.5

Standard error of the above failed command:
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2021.11/bin/hsp.py", line 4, in
import('pkg_resources').run_script('PICRUSt2==2.4.1', 'hsp.py')
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/pkg_resources/init.py", line 656, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/pkg_resources/init.py", line 1453, in run_script
exec(code, namespace, namespace)
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/PICRUSt2-2.4.1-py3.8.egg/EGG-INFO/scripts/hsp.py", line 145, in
main()
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/PICRUSt2-2.4.1-py3.8.egg/EGG-INFO/scripts/hsp.py", line 121, in main
check_files_exist([args.tree, trait_table])
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/PICRUSt2-2.4.1-py3.8.egg/picrust2/util.py", line 406, in check_files_exist
raise ValueError("This input file was not found: " + missing_files[0])
ValueError: This input file was not found: /home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/PICRUSt2-2.4.1-py3.8.egg/picrust2/default_files/prokaryotic/16S.txt.gz

Could you kindly assist me?
Thanks in advance.

6

Hey Ruiz-Limon,

It looks like the default reference files are missing for some reason!

The first thing I would try is to install the latest version of QIIME 2 and PICRUSt2 - the latest q2-picrust2 was tested to work with v2023.2, so that should work fine.

If you run into this problem again then you will have to install PICRUSt2 from source instead to get around this issue of missing reference files: Installation · picrust/picrust2 Wiki · GitHub

All the best,

Gavin

1 Like
7

Hi Gavin,

Thank you for getting back to me. I’ll give it a try! :blush:

Best regards,
Patricia

8

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